Shared strategies for β-lactam catabolism in the soil microbiome

Abstract

The soil microbiome can produce, resist, or degrade antibiotics and even catabolize them. While resistance genes are widely distributed in the soil, there is a dearth of knowledge concerning antibiotic catabolism. Here we describe a pathway for penicillin catabolism in four isolates. Genomic and transcriptomic sequencing revealed β-lactamase, amidase, and phenylacetic acid catabolon upregulation. Knocking out part of the phenylacetic acid catabolon or an apparent penicillin utilization operon (put) resulted in loss of penicillin catabolism in one isolate. A hydrolase from the put operon was found to degrade in vitro benzylpenicilloic acid, the β-lactamase penicillin product. To test the generality of this strategy, an Escherichia coli strain was engineered to co-express a β-lactamase and a penicillin amidase or the put operon, enabling it to grow using penicillin or benzylpenicilloic acid, respectively. Elucidation of additional pathways may allow bioremediation of antibiotic-contaminated soils and discovery of antibiotic-remodeling enzymes with industrial utility.

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Fig. 1: ABC strains catabolize penicillin as their sole carbon source.
Fig. 2: Evidence for shared strategy for penicillin catabolism among ABC strains.
Fig. 3: paaF and the put operon are necessary for penicillin catabolism in ABC07.
Fig. 4: Put1 is a benzylpenicilloic-acid-hydrolyzing amidase.
Fig. 5: E. coli expression of penicillin amidase or the put operon gives significantly increased growth on penicillinoids.
Fig. 6: Schematics illustrating penicillin catabolic strategies.

Change history

  • 27 December 2018

    In the version of the article originally published, the x axis of the graph in Fig. 4d was incorrectly labeled as “Retention time (min)”. It should read “Reaction time (min)”. The ‘deceased’ footnote was also formatted incorrectly when published. The footnote text itself should include the name of co-author Tara A. Gianoulis in addition to the previous link to her name in the author list through footnote number 10. The errors have been corrected in the HTML and PDF versions of the article.

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Acknowledgements

This work is supported in part by awards to G.D. through the Edward Mallinckrodt, Jr. Foundation (Scholar Award), and from the NIH Director’s New Innovator Award (http://commonfund.nih.gov/newinnovator/), the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK: http://www.niddk.nih.gov/), the National Institute of General Medical Sciences (NIGMS: http://www.nigms.nih.gov/), and the National Institute of Allergy and Infectious Diseases (NIAID: https://www.niaid.nih.gov/) of the National Institutes of Health (NIH) under award numbers DP2DK098089, R01GM099538, and R01AI123394, respectively. T.S.C. received support from a National Institute of Diabetes and Digestive and Kidney Diseases Training Grant through award number T32 DK077653 (P.I. Tarr, Principal Investigator) and a National Institute of Child Health and Development Training Grant through award number T32 HD049305 (K.H. Moley, Principal Investigator). K.J.F. received support from the NHGRI Genome Analysis Training Program (T32 HG000045), the NIGMS Cellular and Molecular Biology Training Program (T32 GM007067), and the NSF as a graduate research fellow (award number DGE-1143954). M.K.G. received support as a Mr. and Mrs. Spencer T. Olin Fellow at Washington University and from the NSF as a graduate research fellow (DGE-1143954). Sequencing through the US Army Edgewood Chemical Biological Center was supported in part through funding provided by the Transformational Medical Technologies Initiative of the Defense Threat Reduction Agency, US Department of Defense. The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies. We are thankful to J. Hoisington-Lopez in the Center for Genome Sciences and Systems Biology at Washington University in St. Louis School of Medicine for Illumina sequencing support, T. Wencewicz and B. Evans for their useful discussions regarding biochemistry and LC–MS and members of the Dantas lab for general helpful discussions regarding the manuscript.

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T.S.C., A.S., T.A.G., M.O.A.S., and G.D. conceived of experiments and design of work. T.S.C., B.W., A.S., and T.A.G. performed in vitro, microbial, and transcriptomic experiments. L.A.J., S.M.B., C.N.R., E.W.S., and H.S.G. sequenced strain genomes. T.S.C., A.S., T.A.G., K.J.F, and M.K.G. provided analyses. Article drafting was performed by T.S.C. with critical revision performed by T.S.C., B.W., A.S., K.J.F, M.K.G., M.O.A.S., and G.D.

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Correspondence to Gautam Dantas.

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Supplementary Tables 1–4, Supplementary Figures 1–8

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RNA-seq count dataset

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Crofts, T.S., Wang, B., Spivak, A. et al. Shared strategies for β-lactam catabolism in the soil microbiome. Nat Chem Biol 14, 556–564 (2018). https://doi.org/10.1038/s41589-018-0052-1

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